which are you talking about? the manga or the light novels? the first series is different because the manga wasn't finished and the mangaka wanted the anime to have a different ending. the newer seriers brotherhood had to skip through some material because the first season of the original series covered the lab 5 arc as well. after that it is all new material 100%. some of the omake and light novels have been adapted to episodes, like the tringham brothers episode was adapted from the novel land of sand. any other differences are probably artistic license or for the sake of convenience.